Abstract: Taking naturally growing grass (NG) as comparison, high-throughput sequencing technique was adopted to examine the effects of Lolium perenne (LP), Trifolium repens (TR), Vulpia myuros (VM), and Vicia villosa (VV) cultivation on soil microbial community in apple orchard of Yanggu County, Shandong Province, and the correlations of soil microbial community with soil nutrient and physicochemical property. The results showed that LP increased the relative abundance of Alternaria and Aspergillus in soil, TR increased that of Gibberella, VM increased Aureobasidium and Chaetomium, and VV increased probiotics such as Nitrososophaera and Metarhizium. However, the quantity of pathogenic bacteria Ralstonia was improved in NG treatment. Results from Spearman correlation analysis showed that the abundance of Bacillus was significantly positively correlated with the concentration of soil organic matter. The abundance of Aspergillus was significantly negatively correlated with available phosphorus, available potassium, CEC, and organic matter. The abundance of Metarhizium was significantly positively correlated with soil pH and CEC. Planting VV between rows of apple orchards, and enhancing the soil organic matter and nutrients content in a certain extent, helped to improve soil micro-ecological environment.